Scripts: R scripts and Mr. Bayes command block to produce all simulated datasets, run analyses, produce output trees, and generate tables, graphs and plots.

Sim1_Data&OutputTrees: simulated datasets and output trees from (simplistic) Simulations 1

Sim2_Data: simulated datasets from (complex) Simulations 2

Sim2_OutputTrees: output trees from (complex) Simulations 2

Sim2_PerformanceResults: All output tables, graphs, and tree plots using two different tree metrics from (complex) Simulations 2

Treespace: All output tables and graphs for tree space analyses

Empirical_Analyses: Empirical dataset from Mitchel et al. (2014) on Palaeognathae with output trees 

